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= Overview of the <code>findCigars</code> function of <code>bamUtil</code> =
= Overview of the <code>findCigars</code> function of <code>bamUtil</code> =
The <code>findCigars</code> option on the [[bamUtil]] executable outputs just the reads that contain any of the specified CIGAR operations.
The <code>findCigars</code> option on the [[bamUtil]] executable outputs just the reads that contain any of the specified CIGAR operations.
= Usage =
./bam findCigars --in <inputFile> --out <outputFile.sam/bam/ubam (ubam is uncompressed bam)> [--cinsert] [--cdel] [--cpad] [--cskip] [--chardClip] [--csoftClip] [--nonM] [--noeof] [--params]
= Parameters =
= Parameters =
--params : print the parameter settings
--params : print the parameter settings
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{{PhoneHomeParamDesc}}
== Required Parameters ==
{{InBAMInputFile}}
{{OutBAMOutputFile}}
== CIGAR Selection Parameters (<code>--cinsert</code>, <code>--cdel</code>, <code>--cpad</code>, <code>--cskip</code>, <code>--chardClip</code>, <code>--csoftClip</code>, <code>--nonM</code>) ==
Use these parameters to select which reads to keep based on the cigar. By default, none of these options are on, so no reads would be kept.
Keep any read with any of the specified cigar operators (multiple can be specified and a read that has any of them will be kept):
* --cinsert : insertion
* --cdel : deletion
* --cpad : pad
* --cskip : skip
* --chardClip : hard clip
* --csoftClip : soft clip
Use --nonM to keep any read that has a non M/X/= Cigar operator.
= Usage =
== Optional General Parameters ==
{{paramsParameter}}
{{noeofBGZFParameter}}
{{PhoneHomeParameters}}
= Return Value =
= Return Value =
